The README for Song and Silence states that if you've kitted Imoen or Nalia as Adventurers in the NPC Kitpack, that mod will update them to its own version of the Adventurer kit. This in fact happens; the relevant CRE files are tagged with A!Adventurer as they should be. But when either Imoen or Nalia join your party, you'll find that they've reverted back to their NPC kitpack versions. This is due to the override scripts that have code like so for Imoen:

IF
InParty(Myself)
Global("IKNPCKit","LOCALS",0)
Class(Myself,MAGE_THIEF)
THEN
RESPONSE #100
AddKit(IK_ADVENTURER)
ReallyForceSpellRES("IKitImo1",Myself) // No such index
SetGlobal("IKNPCKit","LOCALS",1)
END

There's slightly different but equivalent code of you've asked for them to have specialist mage kits as well. Affected scripts are:

BGIMOEN.BCS

IMOEN.BCS

IMOEN2.BCS

IMOE25.BCS

NALIA.BCS

NALI25.BCS

I've taken to commenting out the offending sections, which seems to work well enough.